[ensembl-dev] Targetted Genewise
Alex Humberto Di Genova Bravo
digenova at gmail.com
Mon Nov 1 19:23:44 GMT 2010
Dear Amonida:
Thank you very much for your help, Well, Pmatch and BestPmatch were
run before the Targetted genewise. I am using the last ensembl code and
I run the analisys using the Job_submition.pl script with the
following parameters:
perl job_submission.pl $VARS -logic_name TargettedGenewise
where VARS is an environment variable with the following parameters
VARS="-dbhost bio-0.dim.uchile.cl -dbuser gendb -dbpass pass -dbname
test_ensembl "
Also I tested the TargettedGenewise with test_RunableDB script:
perl test_RunnableDB $VARS -logic_name TargettedGenewise -input_id
chromosome:NCBI36:1:1:986048:1
but I get the same error, I am sure that the error is after run
genewise, looking at the code I think that
the error occur in the Filtering stage of the transcripts.
My TMP directory contains the following files:
pep.28638.3793.fa results.21492.78903.out seq.17394.13803.fa
tempblast.11900 .........
where pep.28638.3793.fa contains the protein mapped with PMATCH and
BESTPMATCH
seq.17394.13803.fa is the genome fragment, tempblast.11900 is the
directory that contains the
wutblastn result and results.21492.78903.out contains the genewise
result.
Thank in advance
Alex
El 01-11-2010, a las 2:56, Amonida Zadissa escribió:
> Dear Alex,
>
> Could you please let us know how you got the error messages. Several
> possibilities come to mind that might have caused the error.
>
> 1. I assume you ran Pmatch and BestPmatch prior to running
> TargettedGenewise. If you have run these, did you specify where your
> BestPmatch features are stored? The variable PAF_SOURCE_DB in the
> config file should be pointing to the database that holds these
> features.
> 2. Did you use the latest Ensembl API?
> 3. Did you run the test_RunnableDB script in ensembl-analysis/
> scripts/test_RunnableDB?
> 4. How did you run the analysis? Could you tell us the rulemanager
> command that you used.
>
> Let us know how you get on solving the problem.
>
> Best regards,
> Amonida
>
>
> On 28/10/10 20:43, Alex Humberto Di Genova Bravo wrote:
>> Dear Ensembl Developers:
>>
>> I am working in a local installataion of the ensembl pipeline. I
>> complete the raw compute stage of
>> the pipeline without problem and now
>> I trying to run the Targetted stage of the gene build process, This
>> is my actual configuration of
>> this analisys:
>>
>> TargettedGenewise => {
>>
>> PAF_LOGICNAMES => ['BestPmatch'],
>> OUTPUT_BIOTYPE => 'targetted',
>> GENEWISE_PARAMETERS => {
>> # pass parameters go genewise here, i.e. -program =>"/usr/local/
>> ensembl/bin/genewiseXXX"
>> # for more options which can be passed see Runnable/Genewise.pm
>> #-program=>'/genoma/gendb/ensembl/bin/genewise'
>> #-endbias => 1,
>> -gene => '/genoma/gendb/ensembl/lib/cfgwise/human.gf',
>> -matrix => '/genoma/gendb/ensembl/lib/cfgwise/BLOSUM80.bla',
>> -codon => '/genoma/gendb/ensembl/lib/cfgwise/codon.table',
>> -gap => 20,
>> -extension => 8,
>> -splice_model => 1
>> },
>> MINIGENEWISE_PARAMETERS => {
>> -terminal_padding => 20000,
>> -exon_padding => 200,
>> -minimum_intron => 1000,
>> },
>> MULTIMINIGENEWISE_PARAMETERS =>{
>> -minimum_feature_length => 50,
>> },
>> FILTER_PARAMS => {
>> -max_exon_length => '20000',
>> -multi_exon_min_coverage => '25',
>> -single_exon_min_coverage => '80',
>> -max_intron_length => '200000',
>> -min_split_coverage => 95,
>> -max_low_complexity => 101,
>> },
>> SEQFETCHER_PARAMS => {
>> -db => ['/genoma/gendb/ensembl/testgenome/protein_danio_rerio_index']
>> },
>> BLASTMINIGENEWISE_PARAMETERS => {},
>> LIMIT_TO_FEATURE_RANGE => 1,
>> FEATURE_RANGE_PADDING => 20000,
>> },
>>
>> Stored in the Config file of BlasMiniGenewise Module, The binaries
>> (SEQFETCHERT , xdformat,
>> wutblastn and genewise) run in my test genome without
>> problems, I confirm that comenting the lines on the
>> runnables(Blast.pm, genewise.pm and
>> BlastMiniGenewise.pm) that delete the temporal files.
>> Currently my databases configuration comprise the REFERENCE_DB and
>> a separate GENEWISE_DB as is
>> specified in the gene build readme or in
>> databases readme.
>>
>> I genereta the input IDs for TargettedGenewise on slice level of
>> 1MB using the make_input_id script,
>> So When I check the job error there is a lot of warnings that end
>> whit an error of undefined seq:
>>
>>
>> -------------------- WARNING ----------------------
>> MSG: Transcript has no translation, or no start exon - maybe a
>> pseudogene?
>> FILE: Tools/GeneBuildUtils/TranscriptUtils.pm LINE: 1921
>> CALLED BY: Analysis/RunnableDB/BlastMiniGenewise.pm LINE: 648
>> Ensembl API version = 60
>> ---------------------------------------------------
>> 1
>> -------------------- WARNING ----------------------
>> MSG: Transcript has no translation, or no start exon - maybe a
>> pseudogene?
>> FILE: Tools/GeneBuildUtils/TranscriptUtils.pm LINE: 1921
>> CALLED BY: Analysis/RunnableDB/BlastMiniGenewise.pm LINE: 648
>> Ensembl API version = 60
>> ---------------------------------------------------
>> Non-coding transcript does not have -1 phases at
>> /genoma/gendb/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/
>> Tools/GeneBuildUtils/TranscriptUtils.pm
>> line 466.Can't call method "seq" on an undefined value at
>> /genoma/gendb/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/
>> Tools/GeneBuildUtils/TranslationUtils.pm
>> line 201.
>>
>> RUNNING: Lost the will to live Error
>> Job 16910 failed: [
>> -------------------- EXCEPTION --------------------
>> MSG: Problems running BlastMiniGenewise for
>> chromosome:NCBI36:1:25637249:26623296:1 [Can't call
>> method "seq" on an undefined value at
>> /genoma/gendb/ensembl/ensembl-analysis/modules/Bio/EnsEMBL/Analysis/
>> Tools/GeneBuildUtils/Tr
>> anslationUtils.pm line 201.
>> ]
>>
>> STACK Bio::EnsEMBL::Pipeline::Job::run_module
>> /genoma/gendb/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
>> Job.pm:634
>> STACK (eval) /genoma/gendb/ensembl/ensembl-pipeline/modules/Bio/
>> EnsEMBL/Pipeline/runner.pl:219
>> STACK main::run_jobs_with_lsfcopy
>> /genoma/gendb/ensembl/ensembl-pipeline/modules/Bio/EnsEMBL/Pipeline/
>> runner.pl:218
>> STACK toplevel /genoma/gendb/ensembl/ensembl-pipeline/modules/Bio/
>> EnsEMBL/Pipeline/runner.pl:128
>> Ensembl API version = 60
>> ---------------------------------------------------
>> ]Finished job 16910
>>
>>
>> and there is no feature stored in GENEWISE_DB, this happend for all
>> of my jobs, Any suggestion or
>> advice will be very usefull
>> for me.
>>
>>
>> Thank in advance
>>
>> Alex Di Génova.
>> Ingeniero en Bioinformatica.
>> Laboratorio de Bioinformatica y Matemática del Genoma.
>> Centro de Modelamiento Matemático.
>> Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile.
>> Avenida Blanco Encalada 2120, Piso 6.
>>
>>
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>> Dev at ensembl.org
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>>
>
>
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